2PID Ligase date Apr 13, 2007
title Crystal Structure Of Human Mitochondrial Tyrosyl-Trna Synthe Complex With An Adenylate Analog
authors L.Bonnefond, M.Frugier, E.Touze, B.Lorber, C.Florentz, R.Giege, C. J.Rudinger-Thirion
compound source
Molecule: Tyrosyl-Trna Synthetase
Chain: A, B
Fragment: Residues 28-375
Synonym: Tyrosine-Trna Ligase, Tyrrs
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Yars2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Top10
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe70-Mt-Tyrrs-[Delta]S4
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.244
length a length b length c angle alpha angle beta angle gamma
54.000 62.400 194.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand YSA enzyme Ligase E.C. BRENDA
A, B

Primary referenceCrystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features., Bonnefond L, Frugier M, Touze E, Lorber B, Florentz C, Giege R, Sauter C, Rudinger-Thirion J, Structure. 2007 Nov;15(11):1505-16. PMID:17997975
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (2pid.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 2PID
  • CSU: Contacts of Structural Units for 2PID
  • Likely Quarternary Molecular Structure file(s) for 2PID
  • Structure Factors (281 Kb)
  • Retrieve 2PID in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PID from S2C, [Save to disk]
  • Re-refined 2pid structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PID in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2PID
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2PID, from MSDmotif at EBI
  • Fold representative 2pid from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pid_B] [2pid_A] [2pid]
  • SWISS-PROT database: [Q9Y2Z4]
  • Domain organization of [SYYM_HUMAN] by SWISSPFAM
  • Other resources with information on 2PID
  • Community annotation for 2PID at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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